Dear all,
I’m a French student working on molecular dynamics and I have some trouble using the neb command in LAMMPS.
I’m trying to calculate the energy barrier in Titanium HCP of an Hydrogen atom from a tetrahedral site to another. My script works fine (I mean I don’t get errors) but when i plot the Energy Barrier Forward (EBF) versus the Total Reaction Coordinate (RDT), I get nonsense.
Moreover, It seems like the landmark used in file-style final is not the same as the one used in create atoms ( same coordinates do not relate the same position).
I read examples on neb provided by lammps but it didn’t helped me. Please help me to understand what I’m doing wrong using this neb command.
Here’s my script, followed by he file used in file-style final in neb command.
Thanks for your help,
CHEVALIER David
in.neb :
variable temperature equal 0
variable concentration equal 0.01
variable latparamTi equal 2.951000
variable tetrax equal 1
variable tetray equal 1/3
variable tetraz equal 1/8
------------------------ INITIALIZATION ----------------------------
units metal
dimension 3
boundary p p p
atom_style atomic
atom_modify map array
atom_modify sort 0 0
variable latparamAl equal 8
#Time-step parameter
variable dt equal 0.001
Temperature ramp parameter
variable tdamp equal 100*${dt}
Pressure parameter
variable pdamp equal 1000*${dt}
----------------------- ATOM DEFINITION ----------------------------
lattice hcp ${latparamTi}
region box block 0 10 0 10 0 10
create_box 2 box
create_atoms 1 region box
create_atoms 2 single {tetrax} {tetray} ${tetraz}
mass 2 1.00794
mass 1 47.88
group H type 2
group Ti type 1
region nebr sphere {tetrax} {tetray} ${tetraz} 2 side in
group neb region nebr
------------------------ FORCE FIELDS ------------------------------
pair_style hybrid eam/alloy/opt table linear 3201
pair_coeff * * eam/alloy/opt Farkas_Nb-Ti-Al_1996.eam.alloy Ti NULL
pair_coeff 2 2 table pair_HTi.txt Effpair_HH 6.5
pair_coeff 1 2 table pair_HTi.txt Effpair_HTi 6.5
neighbor 2.0 bin
neigh_modify delay 0 check yes
------------------------- SETTINGS ---------------------------------
set up neb run
variable u uloop 20
fix freeze Ti setforce 0.0 0.0 0.0
displace_atoms H random 0.1 0.1 0.1 123456
minimize 1.0e-6 1.0e-4 1000 10000
reset_timestep 0
dump events neb custom 100 dump.neb.test.$u id type x y z
fix 1 all neb 1.0 #parallel ideal #end last/efirst/middle 1
thermo 10
timestep 0.01
min_style quickmin
#neb 0.0 0.01 100 100 10 final dump.finalneb.lammpstrj
neb 0.0 0.01 1000 1000 10 final dump.finalneb.lammpstrj
File for file-style final :
1
4001 6 0.3333 0.125